What Is a PDB File?

PDBs store database information

What to Know

  • Some PDB files are program database files.
  • Open one with a text editor or a program like Geneious.
  • Convert to another format with the same program that opens your specific database file.

This article explains what a PDB file is, how to open one, and how to convert one to a different format.

Definition of a PDB File

A file with the PDB file extension is most likely a program database file that's used to hold debugging information about a program or module, like a DLL or EXE file. They're sometimes called symbol files.

The file maps various components and statements in source code to its final compiled product, which the debugger can then use to find the source file and the location in the executable at which it should stop the debugging process.

Some PDB files might instead be in the Protein Data Bank file format. These are plain text files that store coordinates regarding protein structures.

Other PDB files might be created in the Palm Database or PalmDOC file format and used with the PalmOS mobile operating system; some files in this format use the .PRC file extension instead. Yet another format that uses this same extension is Tanida Demo Builder.

Screenshot of several PDB files in Windows 10 that open with Notepad

How to Open a PDB File

Different programs use their own PDB file to store data in some sort of structured database format, so each application is used to open its own type.

Geneious, Quicken, Visual Studio, and Pegasus are just a few examples of programs that might use the file as a database file. Radare and PDBparse might also work.

Some PDB files are stored as plain text, like Geneious' Program Debug Database files, and are completely human-readable if opened in a text editor. You can open this kind of PDB file with any program that can read text documents, like the built-in Notepad program in Windows. Some other compatible viewers and editors include Notepad++ and Brackets.

Other PDB files aren't text documents and are only useful when opened with the program that it's intended for. For example, if yours is related in some way to Quicken, then try using that software to view or edit it. Visual Studio expects to see a PDB file in the same folder as the DLL or EXE file.

You can view and edit Protein Data Bank files in Windows, Linux, and macOS with Avogadro. These programs can open the file, too: Jmol, RasMol, QuickPDB, and USCF Chimera. Since these are plain text, you can open one in a text editor as well.

Palm Desktop should be able to open this file if it's in the Palm Database file format, but you might have to first rename it to have the PRC file extension for that program to recognize it. Calibre is another option.

To open a PalmDOC PDB file, try STDU Viewer.

Tanida Demo Builder opens files in that format.

How to Convert a PDB File

Program database files can most likely not be converted to a different file format, at least not with a regular file converter tool. Instead, if there is any application that can convert this kind of file, it'd be the same program that can open it.

For example, if you need to convert your database file from Quicken, try using that program to do it. This type of conversion, however, is probably not only of little use but also not supported in these database applications (i.e., you probably don't need to convert this kind of PDB file to any other format).

Protein Data Bank files can be converted to other formats with MeshLab. To do this, you might have to first convert it to WRL with PyMOL from the File > Save Image As > VRML menu, and then import the WRL file into MeshLab and use the File > Export Mesh As menu to ultimately convert the PDB file to STL or another file format.

If you don't need the model to be in color, you can export the file directly to STL with USCF Chimera (the download link is above). Otherwise, you can use the same method as above (with MeshLab) to convert PDB to WRL with USCF Chimera and then export WRL to STL with MeshLab.

To convert PDB to PDF or EPUB, if you have a PalmDOC file, is possible in a number of ways, but the easiest is probably to use an online converter like Zamzar. You can upload your file to that website to have the option of converting it to those formats as well as to AZW3, FB2, MOBI, PML, PRC, TXT, and other eBook file formats.

To convert one to the FASTA format can be done with Meiler Lab's online PDB to FASTA converter.

It's also possible to save this file to CIF (Crystallographic Information format) online using PDBx/mmCIF.

Still Can't Open It?

Files that aren't opening with any of the tools from above, probably aren't actually PDB files. What might be happening is that you're misreading the file extension; some formats use a suffix that closely resembles PDB, when they're really unrelated and don't work the same.

For example, a PDF file is a document file, but most of the programs from above will not render the text and/or images correctly if you try to open one with these software programs. The same is true for other files with similarly spelled file extensions, like DBF, DB, ADP, PD, PDE, PDC, PDO, and WPD files.

PBD is another that belongs to the EaseUS Todo Backup program and is therefore only useful when opened with that software.

If you don't have a PDB file, research the file extension that your file does have so that you can find the appropriate program that opens or converts it.

Advanced Reading on PDB Files

You can read a lot more about program database files from GitHub and Wintellect.

There's more to learn about Protein Data Bank files, too; see Worldwide Protein Data Bank and RCSB PDB.

  • How do I fix it when Visual Studio is unable to find or open PDB files?

    If you see a message stating that Visual Studio cannot find or open the PDB file, try using Visual Studio's debugging tool. Go to Tools > Options > Debugging > Symbols and select Microsoft Symbol Servers.

  • How do I open a PDB file on Android?

    Use a third-party file reader. Download the Cool Reader app or any other PDB file-supported reader on Google Play.

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